I had already been warned about writing “too much” about two arrested journalists, and my last two articles – one on the prime minister’s war on journalists, and the other on the rights of the Kurdish people – were considered controversial. So the conversation was not unexpected.

But then came the readers’ uproar on Twitter. Some of my fellow columnists too protested about the political motives behind my firing – while government supporters said: “She deserved it!” .

It took me several days to see the bigger picture. But when I did I realised it was all connected to three lost colleagues: one dead and two imprisoned and a story that started five years ago.

On 19 January 2007 the Armenian journalist Hrant Dink was shot dead in broad daylight in front of his office in Istanbul. A man who was just 17 years old at the time of the killing was found guilty of his murder five years later. Yet from day one it was obvious to those who know the history of assassinations in Turkey that this was a political killing.

The murder occurred just two days before I was supposed to meet Hrant to discuss a book he wanted me to write about the Armenian diaspora. Instead, I raced to the scene and found myself standing outside his offices in a pool of his blood.

Afterwards I felt deeply guilty for taking the death threats against him too lightly, making me more determined to write Deep Mountain – the book he asked for. I didn’t know it then, but among the 100,000 people who marched at Hrant’s funeral, there were also two others eager to dedicate their work to him: my friends and colleagues Nedim Sener and Ahmet Sık.

During the next four years articles in the newspaper Milliyet pointed to the police’s negligence in the case, the intelligence service concealing evidence, and the fact government departments knew in advance of a murder plot against Dink.

Yet soon it was the author of these reports, Nedim Sener, who was arrested. The arrest came three months after publishing his book The Red Friday – Who broke Dink’s Pen?, which brought together his findings on Dink’s case and linked the murderers with the state. Reporter Ahmet Sık, meanwhile, did not even have time to publish his book on the same subject before he was arrested, on the same day – March 3 2011.

Both men have now been in jail for 11 months and are accused of being members of a terrorist organisation that might have killed Dink. This isErgenekon, a clandestine organisation supposedly consisting of retired generals, journalists and politicians who are said to have planned a string of high profile assassinations to create chaos and lay the ground for a military coup.

The indictment in court said their years of journalistic work were just a cover to hide their real terrorist identity. Open threats from the prime minister, Recep Tayyip Erdogan, against journalists who continued to cover news about their arrested colleagues led to protests against their arrests gradually fading away before Nedim and Ahmet’s first hearing months after they were imprisoned.

But on 27 December, despite fearing arrest, Turkey’s brave journalists started tweeting from the trial. The weak evidence made it clear any one of us reporters could also be arrested and accused of terrorism; because all that linked Ahmet, Nedim and the Ergenekon organisation was an infected Word document in their computers, casual phone conversations and interviews that they carried out for their respective books. The indictment was so ridiculous that it caused constant laughter in the court room.

Before their last hearing of 23 January, five years after his murder, there was a verdict in Dink’s case. The court refused to acknowledge the obvious links between the murderers and the state, leading to a 30,000-person strong demonstration. Three days later, Nedim, during his defence statement, made it clear he believed he was being kept in prison as part of the attempt to conceal evidence in Dink’s case, saying: “Actually it is good that I am still in prison when Hrant’s verdict is delivered.” Not to mention the government’s promotion of all the officers who have alleged ties with the murder.

Ahmet, an expert on paramilitary organisations, had written a book, Army of Imam, exploring how the intelligence service had been infiltrated by the Fethullah Gülen movement – a moderate Islamist network. “As a socialist,” he said in his defence statement, “I find it condescending to be accused of being a member of militarist, nationalist terrorist network, Ergenekon.” For the fifth time, Ahmet and Nedim will be forced to defend themselves in court as the case continues.

The inquiries for Ergenekon started five years ago, and despite thousands being arrested and imprisoned no verdict has been reached. According to freedom of speech advocates, the Ergenekon case, along with the KCK case – against the civil organisation linked to the armed Kurdish movement PKK – has become a handy tool for the government to harass the opposition.

Both use an infamous anti-terrorism law to get rid of government opponents. And a few days before Hrant’s verdict the minister of the interior, Idris Naim Sahin, said: “Terror is a multifaceted phenomenon that includes psychology and art … Sometimes it is on canvas, sometimes in a poem, in daily articles, or even jokes. We know that terrorist cells might include a university chair, an association or a NGO.”

Thanks to this mentality, Turkey is now ranked the 148th of 179 in Reporters Without Border’s press freedom index – just a bit above Afghanistan and slipping down constantly. More importantly the silent fear among journalists is impossible to put into numbers; consider the 3,500 Kurdish and Turkish politicians, the 500 students and the 100 journalists who are now in jail.

Yesterday the prime minister made a statement saying that arrested journalists are not behind bars because of journalism but for their crimes of sexual harassment or terrorism. As Dink said five ago in his last article, we journalists are “like frightened doves”. One killed, two imprisoned, myself unemployed – and as Nedim said in his latest defence statement: “It hurts.”